Here we perform the annotation of the persistent components extracted from the single cell RNASeq dataset of PBMC (GSE132044). On this dataset, we used only 10x v2 data.
The top-contributing genes are shown below for each persistent component. Top-contributing genes of a persistent component are the genes whose weights are below or beyond 3 sd from the mean of the weigths in this persistent component.
## [1] TRUE
We used only MCPcounter gene sets and checked if the persistent components were enriched in these gene sets.
For that, we performed over representation analysis of the top-contributing genes of the positive and negative tails of each persistent component using immunce cell types gene sets.
For each persistent component, a total of 10 gene sets are tested.
There are a total of 8 significant enrichments in positive tails and 4 significant enrichment in negative tails.
There are 5 unique MCPcounter cell types with significant enrichments in the top contributing genes of the positive tails and 3 unique MCPcounter cell types with significant enrichments in their targers in the top_contributing genes of the negative tails.
To decipher the mechnanisms active in the persistent components, we extracted the top_contributing genes in each persistent component and performed over representation analysis as well as gene set enrichment analyses on each persistent component.
Now we can describe each component in details. We used GO, KEGG, MSigDB (http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp) and DO ontology to annotate the persistent components. Results are represented in dotplots, cnetplots and emaplots for both drivers of the positive and negative tails using clusterProfiler (https://bookdown.org/yihui/rmarkdown/html-document.html). If the OR analysis had no enrichment in one or the two tails, no plot is reported.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Gene Ontology.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on KEGG.
Let us now take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on MSigDB catalogues.
Finally, let us take a look at the results of the enrichments of the top-contributing genes of the positive and negative tails based on Disease Ontology.
Top_contributing genes were submitted to over representation analysis. First, we show an overview of the top_contributing genes coming from the postive and negative tails for all components and next, we give details about each component.
We used Dorothea database (Discriminant Regulon Expression Analysis, https://saezlab.github.io/dorothea/, Garcia-Alonso L et al. 2019) to construct gene sets of each of the reported transcription factor. We then checked if the persistent components were enriched in some of these TF gene sets.
For that, we performed over representation analysis of the top-contributing genes of the positive and negative tails of each persistent component using the TF gene sets.
For each persistent component, a total of 361 gene sets are tested.
There are a total of 14 significant enrichments in positive tails and 9 significant enrichment in negative tails.
There are 12 unique TFs with significant enrichments in their targets in the top_contributing genes of the positive tails and 9 unique TFs with significant enrichments in their targets in the top_contributing genes of the negative tails.